抑郁症患者肠道菌群研究

目的研究抑郁症患者肠道微生物群落分布情况。方法选择2017年1月-2018年1月在本院临床心理科就诊的确诊为抑郁症的患者79例,以及同时期在本院体检的健康者80例。收集患者新鲜粪便,利用16SrRNA基因测序技术分析患者肠道菌群。结果对159例粪便标本进行16SrRNA基因测序,共获得1 276 841条有效16SrRNA基因序列,抑郁组Shannon指数明显高于对照组。在门水平,共发现20个细菌门,抑郁患者肠道菌群丰度前3位的分别是厚壁菌门、拟杆菌门、梭杆菌门;在科水平,前3位主要为拟杆菌科、普雷沃氏菌科和瘤胃菌科;在属水平,前3位分别是多形杆菌属、普氏菌属、另枝菌属。对照组肠道菌群丰度前3位的分别是厚壁菌门、拟杆菌门、梭杆菌门;在科水平,前3位主要是拟杆菌科,普雷沃氏菌科和瘤胃菌科;在属水平,前3位分别是多形拟杆菌属、普氏菌属、另枝菌属。抑郁组多形杆菌属、普氏菌属、另枝菌属、栖粪杆菌属、考拉杆菌属丰度明显低于对照组,抑郁组毛螺菌属、副杆菌属、布劳特氏菌属、巨单胞菌属丰度明显高于对照组。抑郁组拟杆菌属和栖粪杆菌属丰度与SDS评分成负相关,毛螺菌属丰度与SDS评分成正相关。结论抑郁症患者病情严重程度与抗炎性细菌拟杆菌属和栖粪杆菌属丰度成反比,与毛螺菌属丰度成正比。     

乌鲁木齐市3~5岁儿童口腔微生物与肠道微生物的构成差异

目的探索乌鲁木齐市3～5岁儿童口腔微生物与肠道微生物的菌群构成及多样性等差异。方法从本团队前期流行病学调查的乌鲁木齐市3～5岁儿童中,按调查时间顺序随机抽取12名儿童。分别收集唾液及粪便样本共计24份,分为口腔微生物组和肠道微生物组。利用16S V3-V4区设计引物来进行PCR扩增,使用MiSeq测序仪进行二代测序,比较两组的微生物构成及多样性差异。结果门水平上:放线菌门(t=5.98,P0.001)、变形菌门(z=20.0,P=0.005)、TM7(z=78.0,P0.001)在口腔中丰度较高;厚壁菌门(z=134.0,P0.001)在肠道中丰度较高。厚壁菌门/拟杆菌门的值在肠道中较大(z=113.0,P=0.017)。属水平上:罗斯菌属、普雷沃菌属、链球菌属为口腔中丰度较高的菌属;粪杆菌属、Ruminococcaceae、拟杆菌属为肠道中丰度较高的菌属(P0.001)。奈瑟菌属、卟啉单胞菌属等仅存在于口腔中。Catenibacterium、肠杆菌属等仅存在于肠道中。菌群功能显示:在细胞运动(z=136.0,P0.001)、碳水化合物代谢(t=-4.71,P0.001)等方面表现出肠道组占优势;在遗传信息的翻译(t=8.17,P0.001)、神经退行性疾病(z=78.0,P0.001)等方面表现出口腔组占优势。结论放线菌门、变形菌门、TM7在口腔中丰度较高;厚壁菌门在肠道中丰度较高。口腔和肠道微生物在菌群功能上差异较大。奈瑟菌属、卟啉单胞菌属、Catenibacterium等可能为某些全身系统性疾病的标志性菌属。     

基于16S rDNA测序绝经综合征抑郁患者肠道菌群结构与功能性分析

目的 通过16S rDNA测序技术对绝经综合征抑郁患者肠道菌群分布、多样性和基因功能进行分析,探讨肠道菌群与绝经综合征抑郁发生的关联。方法 选取2021年6月至2022年3月就诊于我院妇科门诊的绝经综合征抑郁患者19例为观察组（A组）,同期绝经综合征患者10例为对照组（C组）。利用16S r DNA基因测序法对患者肠道菌群进行物种注释分析和功能比较,统计两组肠道菌群分布、多样性和基因功能的变化。结果 两组肠道菌群差异明显。GraPhlAn物种组成图显示,患者肠道菌群总体以厚壁菌门、拟杆菌门、放线菌门和变形菌门组成。在门水平,与C组相比,A组放线菌门、变形菌门相对丰度较低,拟杆菌门相对丰度较高。在属水平,与C组相比,A组拟杆菌属、小杆菌属、巨单胞菌属、Lachnospiracea＿incertae＿se相对丰度较高,而Gemmiger、布劳特菌属、普雷沃菌属、粪球菌属、粪杆菌属、双歧杆菌属相对丰度偏低。进一步在属水平上选取了10种相对丰度差异具有统计学意义的菌群（P<0.05）：韦氏球菌属、消化球菌属、巨单胞菌属、史雷克菌属在A组的相对丰度较高（P<0.05）,柯林斯菌属、C...     

基于16S rRNA基因扩增子测序分析日本囊对虾肠道菌群结构与功能的特征

【背景】肠道菌群在对虾的生理活动中起关键作用。日本囊对虾是我国海水养殖虾类中的主要品种之一,迄今为止有关其肠道菌群结构与功能的研究还鲜有报道。【目的】利用高通量测序技术探究日本囊对虾肠道菌群的组成结构与功能作用,揭示虾体肠道菌群与外源菌群结构间的相关性。【方法】60 d的养殖周期结束后,分别采集日本囊对虾肠道样品(归为虾肠组,n=3)、养殖水体样品(归为水体组,n=3)和对虾饲料样品(归为饲料组,n=3),提取各样品总DNA进行16SrRNA基因扩增子测序,基于生物信息学方法分析与比较样品间的菌群结构特征,并使用PICRUSt软件预测日本囊对虾肠道菌群功能。【结果】3组样品测序共获得822 713条有效序列,抽平处理后可聚类为3 416个OTU。虾肠组样品中有28.49%、59.30%的OTU可以依次在水体组、饲料组样品中检测到。门水平上,虾肠组样品中的优势菌门为变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)和梭杆菌门(Fusobacteria)。水体组、饲料组与虾肠组样品中的优势菌门结构不尽相同,但均由变形菌门和拟杆菌门组成。属水平上,虾肠组样品中的优势菌属包括弧菌属(Vibrio)、另类弧菌属(Aliivibrio)、假交替单胞菌属(Pseudoalteromonas)、假黄棕杆菌属(Pseudofulvibacter)、科尔韦尔氏菌属(Colwellia)、小纺锤状菌属(Fusibacter)、发光杆菌属(Photobacterium)、脱硫弧菌属(Desulfovibrio)、嗜冷杆菌属(Psychrobacter)以及弓形杆菌属(Arcobacter)。水体组和饲料组中检出的核心菌属结构与虾肠组相比有明显差异,其中海命菌属(Marivita)和假单胞菌属(Pseudomonas)分别为养殖水体及对虾饲料样品中的最优势菌属。PICRUSt预测结果显示,日本囊对虾肠道菌群的基因功能主要与新陈代谢类功能有关,包含氨基酸代谢、碳水化合物代谢与能量代谢等。【结论】日本囊对虾肠道菌群与其他种类对虾肠道菌群的结构间存在共性,其形成在一定程度上受到了外源菌群的干预,并在虾体的日常代谢活动中发挥了一定的作用。     

高通量测序研究浓香型酒醅的细菌菌群多样性及共变性

高通量测序研究河南三个不同酒厂的浓香型酒醅的细菌微生物菌群,逐次在门、纲、目、科和属5个水平上分析入窖酒醅和出窖酒醅的菌群多样性,探究酒醅发酵后菌群的共性变化规律。结果表明:浓香型酒醅在门水平上的优势菌为厚壁菌门、变形菌门、放线菌门、拟杆菌门、异常球菌 栖热菌门。在属水平上的优势菌有乳杆菌属、肠杆菌属、短波单胞菌属、克罗彭施泰特氏菌属、节杆菌属、糖多孢菌属、葡萄球菌属。浓香型酒醅发酵后细菌菌群的物种多样性降低,厚壁菌门、杆菌纲、乳杆菌目、乳杆菌科、乳杆菌属的相对丰度增加,而变形菌门、γ 变形菌纲、肠杆菌目、肠杆菌科、肠杆菌属的相对丰度降低。高通量测序研究充分展示了浓香型酒醅的细菌菌群多样性,显示了浓香型酒醅发酵后细菌菌群的共性变化规律。     

七氟菊酯和溴氰菊酯对棉铃虫肠道菌群的影响

【目的】本研究旨在探究拟除虫菊酯类杀虫剂对棉铃虫Helicoverpa armigera幼虫肠道菌群结构及代谢的影响,丰富对杀虫剂作用机理的认识。【方法】分别对棉铃虫2和3龄幼虫饲喂普通人工饲料(对照组, SS)、含2%七氟菊酯(Ⅰ型拟除虫菊酯)粉剂饲料(七氟菊酯处理组,Te)和含2.5%溴氰菊酯(Ⅱ型拟除虫菊酯)乳油饲料(溴氰菊酯处理组, DM),然后提取3龄幼虫肠道菌群基因组DNA;利用Illumina MiSeq二代高通量测序技术对肠道细菌的16S rDNA的V3-V4变异区进行测序,分析其肠道细菌的多样性和丰富度;利用qPCR验证16S rDNA测序分析结果。取2和3龄幼虫肠道,匀浆后进行Biolog-Eco实验,分析肠道细菌对Eco板上31种碳源的代谢情况。【结果】16S rDNA测序结果表明,棉铃虫3龄幼虫肠道细菌主要是厚壁菌门(Firmicutes)、变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)和蓝藻菌门(Cyanobacteria)。与对照组相比,溴氰菊酯处理组和七氟菊酯处理组的棉铃虫幼虫肠道细菌的α多样性指数没有显著性改变,但是菌群结构发生了变化：在门水平,拟杆菌门的相对丰度减少,厚壁菌门和蓝藻菌门的相对丰度增加,qPCR验证结果亦支持16S rDNA测序分析的这个结果;在属水平,拟杆菌属Bacteroides、普氏菌属Prevotella和假单胞菌属Pseudomonas等的相对丰度降低,狭义梭菌属Clostridium sensu stricto 1、埃希菌属-志贺氏菌属Escherichia-Shigella和盐单胞菌属Halomonas等的相对丰度增加,其中盐单胞菌属Halomonas的相对丰度显著增加。Biolog-Eco结果表明,与对照组相比,溴氰菊酯处理组中2龄幼虫对羧酸类碳源的代谢能力下降;溴氰菊酯处理组和七氟菊酯处理组中3龄幼虫对DL-α-磷酸甘油、肝糖和L-苯丙氨酸等碳源的利用能力下降。【结论】结果显示,拟除虫菊酯类杀虫剂对棉铃虫肠道菌群的结构和代谢能力有明显影响,拟除虫菊酯类杀虫剂使棉铃虫肠道有益菌的相对丰度下降,而使致病菌的相对丰度增加。短时间拟除虫菊酯处理未造成抗药性菌群的丰度增加。qPCR检测结果与16S rDNA测序分析结果相似。Ⅰ型和Ⅱ型拟除虫菊酯类杀虫剂对棉铃虫肠道菌群结构和代谢功能的影响不同。     

高通量测序方法分析两种草食性淡水螺肠道菌群多样性

淡水螺是水生态系统中重要的生物类群，也是多种寄生虫的中间宿主。肠道菌群在动物能量代谢和抵抗病原体方面起着重要作用。本文分析了耳萝卜螺Radix auricularia和三旋卷丽螺Planorbella trivolvis肠道菌群的多样性。结果表明：在门水平上，耳萝卜螺有23个菌门，以变形菌门 (Proteobacteria，33.63%)、蓝细菌门(Cyanobateria，15.33%)、绿弯菌门 (Chloroflexi，13.95%) 和放线菌门 (Actinobacteria，12.99%)为主；三旋卷丽螺有13个菌门，以变形菌门 (54.88%)、拟杆菌门 (Bacteroidetes，28.49%) 和放线菌门 (7.65％) 为主。属水平上，耳萝卜螺有厚皮藻属Pleurocapsa、硫网菌属Thiodictyon、纤毛菌属Leptotrichia及类诺卡氏菌属Nocardioides等445个属；三旋卷丽螺有Cloacibacterium、OM60NOR5_clade、假单胞菌属Pseudomonas及红杆菌属Rhodobacter等238个属。有93个菌属为两种螺的共有核心菌群 (所有样本中都存在)，其中27个菌属丰度大于0.5%。两种螺肠道菌群结构差异显著 (P=0.027)。PICRUSt功能预测分析表明，两种螺肠道菌群KEGG功能组成相似，氨基酸代谢、碳水化合物代谢及膜转运丰度较大。综上，两种草食性淡水螺肠道菌群多样性较高且差异显著，但有数量较多的共有核心菌群。     

老年阿尔茨海默病患者肠道微生态改变及其与认知功能的关系探讨

目的探讨老年阿尔茨海默症患者肠道微生态结构与认知功能的关系。方法将2016年7月-2019年5月医院收治的86例老年阿尔茨海默病患者和73例健康志愿者,分别记为研究组和对照组。采用简易精神状态评价量表(MMSE)进行评分评价两组认知功能,采用高通量测序检测两组肠道微生物多样性。比较两组肠道微生物多样性与MMSE评分,并比较研究组中认知功能正常者与障碍者肠道微生物结构;采用Pearson相关性分析法探讨肠道微生物结构与认知功能障碍者的相关性。结果研究组肠道菌群Chao1指数、Shannon指数、放线菌门、拟杆菌门、放线菌科、乳杆菌科、拟杆菌科、双歧杆菌属、乳杆菌属、拟杆菌属、MMSE评分均低于对照组(均P0.05);研究组厚壁菌门、变形菌门、子囊菌门、梭菌科、假单胞菌科、葡萄球菌科、肠杆菌科、隐球酵母科、梭状芽孢杆菌属、假单胞菌属、葡萄球菌属、变形杆菌属、假丝酵母菌属相对丰度均高于对照组(均P0.05);研究组中认知功能障碍发生率为70.93%,且认知功能障碍者肠道菌群Chao1指数、Shannon指数,门、科、属水平相对丰度与认知功能正常者对比和上述结果一致;研究组与对照组肠道拟杆菌门、子囊菌门、拟杆菌科、梭状芽胞杆菌属、假丝酵母菌属、放线菌门、乳杆菌属、拟杆菌属相对丰度差异具有统计学意义(均P0.05);研究组认知功能障碍与认知功能正常者肠道未分类拟杆菌门、子囊菌门、假单胞菌属、拟杆菌属、变形杆菌属、梭状芽孢杆菌属、拟杆菌门、拟杆菌科、假丝酵母菌属相对丰度差异具有统计学意义(均P0.05);研究组中肠道菌群Chao1指数、Shannon指数,放线菌门、拟杆菌门、放线菌科、乳杆菌科、拟杆菌科、双歧杆菌属、乳杆菌属、拟杆菌属相对丰度与MMSE评分均呈正相关,厚壁菌门、变形菌门、子囊菌门、梭菌科、假单胞菌科、葡萄球菌科、肠杆菌科、隐球酵母科、梭状芽孢杆菌属、假单胞菌属、葡萄球菌属、变形杆菌属、假丝酵母菌属相对丰度与MMSE评分均呈负相关。结论老年阿尔茨海默病患者肠道微生物结构存在异常,且认知功能障碍者更加严重,认知功能与肠道微生物相关。     

饥饿及恢复喂食对日本医蛭肠道菌群多样性的影响

为了研究饥饿及恢复喂食对日本医蛭肠道微生物菌群的影响, 采用高通量测序技术分析了正常组、饥饿30d、恢复喂食7d以及恢复喂食14d的日本医蛭肠道微生物菌群特征及多样性的变化。结果显示: 日本医蛭核心菌群门水平上, 主要集中于变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes), 属水平核心菌群有气单胞菌属(Aeromonas)、Mucinivorans属、拟杆菌属(Bacteroides)、丹毒丝菌属(Erysipelothrix)等。饥饿及恢复摄食, 对气单胞菌属、Mucinivorans属在内的核心菌群多样性及丰度产生了一定的影响。本研究为揭示日本医蛭肠道菌群组成以及研究日本医蛭消化道微生物功能奠定了基础。     

阿尔茨海默病早期筛查与肠道菌群变化的相关性

目的研究阿尔茨海默病(AD)早期筛查与肠道菌群(GM)变化的相关性。方法选取郑州市社区符合纳入标准的老年群体,统一接受XYDN-C-V2神经心理评估训练系统测评,依据测评结果分AD组(AD早期,n=40)、对照组(测评结果完全正常,n=40);MiSeq高通量测序检测粪便样本GM,比较α多样性、β多样性、物种门水平及属水平相对丰度,并行LEfSe分析优势菌属,比较差异物种相对丰度,绘制受试者工作特征(ROC)曲线分析差异物种相对丰度对早期AD的筛查价值。结果 AD组Chaol指数、Ace指数、Shannon指数高于对照组,Simpson指数低于对照组(Z=5.667、3.254、4.404、15.866,均P0.05);主坐标分析显示主成分1、主成分2、主成分3贡献率依次为34.6%、10.9%、8.8%,AD组与对照组样本间距离明显,差异显著;与对照组比较,AD组门水平上厚壁菌门、放线菌门、疣微菌门升高,拟杆菌门降低;而在属水平上,AD组拟杆菌属、普雷沃菌属下降,布劳特菌属、梭菌属上升;LEfSe分析显示,AD组属水平上的优势菌属分别为芽生球菌属、瘤胃球菌属2,对照组属水平上的优势菌属为毛罗菌属、Aestuariispira、支原体属;样本中共计筛选出门水平、属水平上相对丰度0.01%的差异物种5个,门水平上AD组拟杆菌门降低,厚壁菌门相对丰度高于对照组;属水平上AD组拟杆菌属、Parasutterella相对丰度低于对照组,Alistipes相对丰度高于对照组;其中拟杆菌属筛查早期AD的曲线下面积值(AUC)最高,以27.54%为Cut-off,其筛查早期AD的敏感度、特异度分别为82.50%、72.50%。结论早期AD患者肠道菌群属水平上拟杆菌属相对丰度可作为AD早期筛查的敏感指标,值得临床重视。     

小龙虾肠道细菌群落多样性及产蛋白酶细菌的筛选

【背景】养殖动物对饲料的消化利用往往与肠道菌群密切相关。【目的】揭示小龙虾肠道细菌群落组成,并从小龙虾肠道筛选产蛋白酶细菌。【方法】在Illumina MiSeq PE300平台对细菌16S rRNA基因V3-V4区进行高通量测序,分析小龙虾肠道细菌群落多样性;通过酪蛋白平板法筛选产蛋白酶细菌并进行分子生物学鉴定。【结果】小龙虾肠道细菌优势门包括变形菌门、软壁菌门、厚壁菌门、拟杆菌门等4个门,累计占比为98.53%;优势属包括柠檬酸杆菌属、支原体科Candidatus_Bacilloplasma暂定属、哈夫尼菌属、肠球菌属、拟杆菌属、梭菌科未分类属、希瓦氏菌属等7个属,累计占比为91.67%。通过酪蛋白平板法筛选的产蛋白酶细菌来自哈夫尼菌属、柠檬酸杆菌属、克雷伯氏菌属和芽孢杆菌属。【结论】小龙虾肠道细菌核心类群在蛋白质消化利用中发挥了重要作用。     

光唇鱼仔稚幼鱼肠道菌群与养殖水体细菌群落的相关性

采用16S rRNA高通量测序,系统研究了光唇鱼(Acrossocheilus fasciatus)仔鱼、稚鱼和幼鱼肠道菌群组成及与同时期养殖水体细菌群落的相关性。研究结果表明,光唇鱼仔鱼、稚鱼和幼鱼的肠道菌群中Chao1指数和Shannon指数均没有显著变化(P>0.05);而随着光唇鱼幼体的发育,养殖水体中Chao1指数和Shannon指数呈现显著下降趋势(P<0.05)。光唇鱼仔鱼和稚鱼肠道菌群中的优势菌门由变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)和厚壁菌门(Firmicutes)组成,而同时期养殖水体中优势菌门为变形菌门;光唇鱼幼鱼肠道菌群中的优势菌门为梭杆菌门(Fusobacteria)和变形菌门,同时期养殖水体中优势菌门由变形菌门、拟杆菌门和梭杆菌门组成。线性回归分析结果显示,随光唇鱼幼体发育,在光唇鱼肠道菌群中变形菌门、厚壁菌门和梭杆菌门相对丰度的时序变化趋势与其在养殖水体中相同。在属水平上,光唇鱼仔鱼、稚鱼肠道菌群中优势菌属均为醋酸杆菌属(Acetobacter),而幼鱼肠道菌群中优势菌属为鲸杆菌属(Cetobacte...     

典型草原区不同生境反硝化菌群的空间特征

【背景】锡林河-河滨湿地-阶地草原是蒙古高原典型草原区代表性的水生-湿生-陆生生境,但不同生境中反硝化菌群的空间分布特征尚不明晰。【目的】阐明典型草原区不同生境反硝化菌群的组成、丰度、空间分布特征及异质性成因。【方法】利用16S rRNA基因测序研究锡林河流域水生、湿生、陆生生境6个样带沉积物/土壤细菌群落组成及相对丰度。基于2014年及以前文献报道的反硝化细菌及16S rRNA基因信息构建参比菌库,筛选生境关联的反硝化菌属。通过典范对应分析等探究反硝化菌群空间异质性成因。【结果】参比菌库包含80种反硝化细菌(65个属),6个样带测序获得的469个细菌属中36个为反硝化细菌属。3种生境共存的反硝化细菌有14个属,其中黄杆菌属(1.65%-14.17%)和噬氢菌属(1.56%-1.69%)是水生和湿生生境共有的优势菌,假单胞菌属(1.85%)是低河漫滩样带的优势菌。空间分布特征显示反硝化菌群沿水生-湿生-陆生生境呈现先升后降的分布趋势,在低河漫滩湿地达到最高值。典范对应分析表明:黄杆菌属、噬氢菌属、气单胞菌属、鞘氨醇单胞菌属等与pH值、水分及沙粒含量呈正相关关系,而芽孢杆菌属、链霉菌属、马杜拉放线菌属等与粘粒、粉粒、有机质、总氮含量等呈正相关关系。【结论】典型草原区反硝化菌群组成及丰度具有明显的生境异质性,低河漫滩湿地是反硝化细菌生长繁殖的最佳生境,由颗粒组成、水分含量和pH等环境因子共同驱动。     

不同健康状态的棘胸蛙肠道菌群结构分析

为探究不同健康状态下棘胸蛙(Paa spinosa, David)肠道菌群结构, 文章对13个健康(Health组)、19个患歪头病(WHD组)和18个患蓝眼病(BED组)的棘胸蛙肠道微生物总DNA进行16S rRNA V4—V5高变区测序。结果显示: 共获得3984个总操作分类单元(Operational taxonomic units, OTUs), 35个门, 80个纲, 155个目, 283个科, 501个属。α多样性结果表明, 健康组的菌群丰富度显著高于患病组(P<0.05), 患病组间的菌群丰富度差异不显著(Chao1指数: Health: 1232.92; WHD: 975.57; BED: 1048.76); 健康和患病组间微生物群落均匀度无显著差异(Shannon指数: 5.27; 5.20; 5.41)。门分类水平分析发现: 厚壁菌门(Firmicutes; 52.08%; 49.57%; 26.48%)、拟杆菌门(Bacteroidetes; 30.55%; 21.93%; 43.02%)和变形菌门(Proteobacteria; 15.55%;10.42%; 5.25%)是棘胸蛙肠道菌群的优势菌门。患病蛙肠道中的优势菌门及其丰度均发生变化, 特别是脱铁菌门(Deferribacteres)在歪头病组和蓝眼病组棘胸蛙肠道中丰度显著上升(0.18%; 14.05%; 22.16%; P<0.05)。属分类水平分析发现: 拟杆菌属(Bacteroides; 29.70%; 16.09%; 21.76%)、丹毒丝菌科中未定义的一个属(An unclassified Erysipelotrichaceae; 21.38%; 6.92%; 4.94%)、毛螺科中未定义的一个属(An unclassified Lachnospiraceae; 12.23%; 15.98%; 4.43%)、柠檬杆菌属(Citrobacter; 10.31%; 6.19%; 1.10%)和真杆菌属(Eubacterium; 9.09%; 4.88%; 0.54%) 是棘胸蛙肠道菌群优势菌属, 但各组间的丰度差异显著; 脱铁菌门的Mucispirillum在患病棘胸蛙肠道中丰度显著上升(0.17%; 13.89%; 21.94% ; P<0.05)。研究表明: 棘胸蛙肠道菌群结构与健康状态相关, 且健康与患病棘胸蛙肠道菌群结构差异显著。     

Towards the human intestinal microbiota phylogenetic core

The paradox of a host specificity of the human faecal microbiota otherwise acknowledged as characterized by global functionalities conserved between humans led us to explore the existence of a phylogenetic core. We investigated the presence of a set of bacterial molecular species that would be altogether dominant and prevalent within the faecal microbiota of healthy humans. A total of 10 456 non-chimeric bacterial 16S rRNA sequences were obtained after cloning of PCR-amplified rDNA from 17 human faecal DNA samples. Using alignment or tetranucleotide frequency-based methods, 3180 operational taxonomic units (OTUs) were detected. The 16S rRNA sequences mainly belonged to the phyla Firmicutes (79.4%), Bacteroidetes (16.9%), Actinobacteria (2.5%), Proteobacteria (1%) and Verrumicrobia (0.1%). Interestingly, while most of OTUs appeared individual-specific, 2.1% were present in more than 50% of the samples and accounted for 35.8% of the total sequences. These 66 dominant and prevalent OTUs included members of the genera Faecalibacterium , Ruminococcus , Eubacterium , Dorea , Bacteroides , Alistipes and Bifidobacterium . Furthermore, 24 OTUs had cultured type strains representatives which should be subjected to genome sequence with a high degree of priority. Strikingly, 52 of these 66 OTUs were detected in at least three out of four recently published human faecal microbiota data sets, obtained with very different experimental procedures. A statistical model confirmed these OTUs prevalence. Despite the species richness and a high individual specificity, a limited number of OTUs is shared among individuals and might represent the phylogenetic core of the human intestinal microbiota. Its role in human health deserves further study.     

Impact of biochar application to soil on the root-associated bacterial community structure of fully developed greenhouse pepper plants

Adding biochar to soil has environmental and agricultural potential due to its long-term carbon sequestration capacity and its ability to improve crop productivity. Recent studies have demonstrated that soil-applied biochar promotes the systemic resistance of plants to several prominent foliar pathogens. One potential mechanism for this phenomenon is root-associated microbial elicitors whose presence is somehow augmented in the biochar-amended soils. The objective of this study was to assess the effect of biochar amendment on the root-associated bacterial community composition of mature sweet pepper (Capsicum annuum L.) plants. Molecular fingerprinting (denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism) of 16S rRNA gene fragments showed a clear differentiation between the root-associated bacterial community structures of biochar-amended and control plants. The pyrosequencing of 16S rRNA amplicons from the rhizoplane of both treatments generated a total of 20,142 sequences, 92 to 95% of which were affiliated with the Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes phyla. The relative abundance of members of the Bacteroidetes phylum increased from 12 to 30% as a result of biochar amendment, while that of the Proteobacteria decreased from 71 to 47%. The Bacteroidetes-affiliated Flavobacterium was the strongest biochar-induced genus. The relative abundance of this group increased from 4.2% of total root-associated operational taxonomic units (OTUs) in control samples to 19.6% in biochar-amended samples. Additional biochar-induced genera included chitin and cellulose degraders (Chitinophaga and Cellvibrio, respectively) and aromatic compound degraders (Hydrogenophaga and Dechloromonas). We hypothesize that these biochar-augmented genera may be at least partially responsible for the beneficial effect of biochar amendment on plant growth and viability.     

A putative G protein-coupled receptor involved in innate immune defense of Procambarus clarkii against bacterial infection

The immune functions of G protein-coupled receptor (GPCR) were widely investigated in mammals. However, limited researches on immune function of GPCRs were reported in invertebrates. In the present study, the immune functions of HP1R gene, a putative GPCR identified from red swamp crayfish Procambarus clarkii were reported. Expression of HP1R gene was significant up-regulated in response to heat-killed Aeromonas hydrophila challenge. HP1R gene silencing mediated by RNA interference significantly enhanced the susceptibility of red swamp crayfish to A. hydrophila and Vibrio alginolyticus, indicating that HP1R was required for red swamp crayfish to defend against bacterial challenge. In HP1R-silenced crayfish, increased bacterial burden and decreased THC in response to bacterial challenge were observed when compared with control crayfish. No significant difference of proPO gene expression was observed between HP1R-silenced and control crayfish after challenge with heat-killed A. hydrophila. However, PO activity in response to bacterial challenge was significantly reduced in HP1R-silenced crayfish. The results collectively indicated that HP1R was an important immune molecule which was required for red swamp crayfish to defend against bacterial infection.     

Broad Diversity and Newly Cultured Bacterial Isolates from Enrichment of Pig Feces on Complex Polysaccharides

One of the fascinating functions of mammalian intestinal microbiota is fermentation of plant cell wall components. Eight-week continuous culture enrichments of pig feces with cellulose and xylan/pectin were used to isolate bacteria from this community. A total of 575 bacterial isolates were classified phylogenetically using 16S rRNA gene sequencing. Six phyla were represented in the bacterial isolates: Firmicutes (242), Bacteroidetes (185), Proteobacteria (65), Fusobacteria (55), Actinobacteria (23), and Synergistetes (5). The majority of the bacterial isolates had ≥97 % similarity to cultured bacteria with sequences in the RDP, but 179 isolates represent new species and/or genera. Within the Firmicutes isolates, most were classified in the families of Lachnospiraceae, Enterococcaceae, Staphylococcaceae, and Clostridiaceae I. The majority of the Bacteroidetes were most closely related to Bacteroides thetaiotaomicron, Bacteroides ovatus, and B. xylanisolvens. Many of the Firmicutes and Bacteroidetes isolates were identified as species that possess enzymes that ferment plant cell wall components, and the rest likely support these bacteria. The microbial communities that arose in these enrichment cultures had broad bacterial diversity. With over 30 % of the isolates not represented in culture, there are new opportunities to study genomic and metabolic capacities of these members of the complex intestinal microbiota.     

Comparison of the Cecal Microbiota of Domestic and Wild Turkeys

The extent to which production methods alter intestinal microbial communities of livestock is currently unknown. As the intestinal microbiota may affect animal health, nutrition, and food safety, a baseline comparison of the cecal communities of domestic and wild turkeys was performed. Oligonucleotide fingerprinting of ribosomal RNA (rRNA) genes (OFRG) of 2,990 16S rRNA clones and dot blot quantification of dominant populations were used to identify the dominant bacterial taxa. Seventy-three percent of all the clones belonged to as yet uncultured genera. However, at a higher phylogenetic level, the OFRG library was composed of 54% Bacteroidetes clones (52% of the domestic library clones, 56% of the wild library clones), 30% Firmicutes clones (33% of the domestic library clones, 32% of the wild library clones), 3% Proteobacteria clones (5% domestic, 2% wild), and 3% Deferribacteres clones (4% domestic, 1% wild). Seven percent of the clones were unidentifiable (6% domestic, 9% wild). Bacteroidetes clones included the genera Alistipes, Prevotella, Megamonas, and Bacteroides. Of the Clostridiales clones, groups IV, IX, and XIV including genera Faecalibacterium, Megasphaera, Phascolarctobacterium, and Papillibacter were predominant. Lactobacillus, Enterococcus, and Streptococcus bacilli were also identified. beta- delta- and gamma-proteobacterial genera included Acinetobacter, Sutterella, and Escherichia. Deferribacteres clones showed high similarity to Mucispirillum schaedleri. Statistical comparison of the domestic and wild turkey clone libraries indicated similar levels of community richness and evenness despite the fact that the two libraries shared only 30% of the total clone operational taxonomic units. Together these results indicate that although high level taxonomic community structure is similar, high-density turkey production causes considerable divergence of the genera found in the ceca of commercial birds from those of their wild counterparts.